Mayors and council leaders from five cities in northern England will hold a summit with business leaders next month to press ministers for more investment.
They are concerned that the government has become less committed to the idea of a Northern Powerhouse after David Cameron and George Osborne departed.
The cities are Liverpool, Newcastle, Sheffield, Manchester and Leeds.
The Department for Transport (DfT) rejected the suggestion that northern England was being short-changed.
The mayors and council leaders said statements from Transport Secretary Chris Grayling in particular had caused them “confusion and concern”.
BBC political correspondent Iain Watson says the flashpoint appears to have been the possibility that not all of the TransPennine rail route will now be electrified.
This has been seen previously as a symbol of the government’s commitment to the Northern Powerhouse.
The local government leaders are hoping their summit will put pressure on ministers to re-commit to the project before Parliament resumes in September.
A DfT spokesman said more than £1bn would be spent on improving the rail infrastructure over the next five years, and a decision would be taken next year on how to improve journey times and increase capacity on the TransPennine route.
He added that northern English cities would also benefit from the investment in the HS2 high-speed rail link.
The summit comes after ministers announced their backing for Crossrail 2 – a proposed north-south rail route across London – but said the Manchester to Newcastle rail link may not be fully electrified despite promises from the previous government.
Mr Grayling and Mayor of London Sadiq Khan are said to be in agreement that there is “no doubt London needs new infrastructure to support its growth and ensure it continues as the UK’s economic powerhouse”.
Mayor of Greater Manchester Andy Burnham said there would be “widespread anger” at the decision to support Crossrail 2.
‘Kick in the teeth’
Shadow cabinet minister Angela Rayner said: “This is a real kick in the teeth again, showing that the Conservatives don’t care about us in the north.
“If we’re really going to be a powerhouse across the north then they’ve got to give us that infrastructure.
“If you look at how much money is spent in London on infrastructure compared to how much money is spent in the North West on infrastructure, there’s thousands of pounds per head difference.”